Auto-generated Pull Request for feat/concurrent-scan

cmd/interpro-cli/main.go

@@ -14,85 +14,146 @@ const (
 	defaultTaxonID      = "44689"
 	defaultOutput       = "interpro_proteins.tsv"
 	defaultPageSize     = 20
+	defaultConcurrency  = 25
 	defaultPollInterval = 15 * time.Second
 	defaultTimeout      = 30 * time.Minute
 )
 
 func main() {
-	cmd := &cli.Command{
+	if err := newCommand().Run(context.Background(), os.Args); err != nil {
+		fmt.Fprintf(os.Stderr, "error: %v\n", err)
+		os.Exit(1)
+	}
+}
+
+func newCommand() *cli.Command {
+	return &cli.Command{
 		Name:  "interpro-manager",
 		Usage: "CLI for interacting with the InterPro protein database",
 		Commands: []*cli.Command{
-			{
-				Name:  "download",
-				Usage: "Fetch InterPro protein records for a taxonomy ID and save to TSV",
-				Flags: []cli.Flag{
-					&cli.StringFlag{
-						Name:    "taxon-id",
-						Aliases: []string{"t"},
-						Value:   defaultTaxonID,
-						Usage:   "NCBI Taxonomy ID",
-					},
-					&cli.StringFlag{
-						Name:    "output",
-						Aliases: []string{"o"},
-						Value:   defaultOutput,
-						Usage:   "Output TSV file path",
-					},
-					&cli.IntFlag{
-						Name:    "page-size",
-						Aliases: []string{"p"},
-						Value:   defaultPageSize,
-						Usage:   "API page size",
-					},
-				},
-				Action: interpro.DownloadAndWrite,
-			},
-			{
-				Name:  "scan",
-				Usage: "Submit protein sequences to InterProScan and save JSON results",
-				Flags: []cli.Flag{
-					&cli.StringFlag{
-						Name:    "fasta",
-						Aliases: []string{"f"},
-						Usage:   "Path to FASTA file (supports multi-FASTA)",
-					},
-					&cli.StringFlag{
-						Name:    "email",
-						Aliases: []string{"e"},
-						Sources: cli.EnvVars("EBI_EMAIL"),
-						Usage:   "Email for EMBL-EBI Job Dispatcher (required)",
-					},
-					&cli.StringFlag{
-						Name:    "output",
-						Aliases: []string{"o"},
-						Value:   ".",
-						Usage:   "Output directory for JSON results",
-					},
-					&cli.StringFlag{
-						Name:    "seq-type",
-						Aliases: []string{"s"},
-						Value:   "p",
-						Usage:   "Sequence type: p (protein) or n (nucleotide)",
-					},
-					&cli.DurationFlag{
-						Name:  "poll-interval",
-						Value: defaultPollInterval,
-						Usage: "How often to check job status",
-					},
-					&cli.DurationFlag{
-						Name:  "timeout",
-						Value: defaultTimeout,
-						Usage: "Maximum time to wait for a single job",
-					},
-				},
-				Action: interpro.Scan,
+			downloadCmd(),
+			scanCmd(),
+			concurrentScanCmd(),
+		},
+	}
+}
+
+func downloadCmd() *cli.Command {
+	return &cli.Command{
+		Name:  "download",
+		Usage: "Fetch InterPro protein records for a taxonomy ID and save to TSV",
+		Flags: []cli.Flag{
+			&cli.StringFlag{
+				Name:    "taxon-id",
+				Aliases: []string{"t"},
+				Value:   defaultTaxonID,
+				Usage:   "NCBI Taxonomy ID",
+			},
+			&cli.StringFlag{
+				Name:    "output",
+				Aliases: []string{"o"},
+				Value:   defaultOutput,
+				Usage:   "Output TSV file path",
+			},
+			&cli.IntFlag{
+				Name:    "page-size",
+				Aliases: []string{"p"},
+				Value:   defaultPageSize,
+				Usage:   "API page size",
 			},
 		},
+		Action: interpro.DownloadAndWrite,
 	}
+}
 
-	if err := cmd.Run(context.Background(), os.Args); err != nil {
-		fmt.Fprintf(os.Stderr, "error: %v\n", err)
-		os.Exit(1)
+func scanCmd() *cli.Command {
+	return &cli.Command{
+		Name:  "scan",
+		Usage: "Submit protein sequences to InterProScan and save JSON results",
+		Flags: []cli.Flag{
+			&cli.StringFlag{
+				Name:    "fasta",
+				Aliases: []string{"f"},
+				Usage:   "Path to FASTA file (supports multi-FASTA)",
+			},
+			&cli.StringFlag{
+				Name:    "email",
+				Aliases: []string{"e"},
+				Sources: cli.EnvVars("EBI_EMAIL"),
+				Usage:   "Email for EMBL-EBI Job Dispatcher (required)",
+			},
+			&cli.StringFlag{
+				Name:    "output",
+				Aliases: []string{"o"},
+				Value:   ".",
+				Usage:   "Output directory for JSON results",
+			},
+			&cli.StringFlag{
+				Name:    "seq-type",
+				Aliases: []string{"s"},
+				Value:   "p",
+				Usage:   "Sequence type: p (protein) or n (nucleotide)",
+			},
+			&cli.DurationFlag{
+				Name:  "poll-interval",
+				Value: defaultPollInterval,
+				Usage: "How often to check job status",
+			},
+			&cli.DurationFlag{
+				Name:  "timeout",
+				Value: defaultTimeout,
+				Usage: "Maximum time to wait for a single job",
+			},
+		},
+		Action: interpro.Scan,
+	}
+}
+
+func concurrentScanCmd() *cli.Command {
+	return &cli.Command{
+		Name:  "concurrent-scan",
+		Usage: "Submit protein sequences to InterProScan concurrently and save JSON results",
+		Flags: []cli.Flag{
+			&cli.StringFlag{
+				Name:    "fasta",
+				Aliases: []string{"f"},
+				Usage:   "Path to FASTA file (supports multi-FASTA)",
+			},
+			&cli.StringFlag{
+				Name:    "email",
+				Aliases: []string{"e"},
+				Sources: cli.EnvVars("EBI_EMAIL"),
+				Usage:   "Email for EMBL-EBI Job Dispatcher (required)",
+			},
+			&cli.StringFlag{
+				Name:    "output",
+				Aliases: []string{"o"},
+				Value:   ".",
+				Usage:   "Output directory for JSON results",
+			},
+			&cli.StringFlag{
+				Name:    "seq-type",
+				Aliases: []string{"s"},
+				Value:   "p",
+				Usage:   "Sequence type: p (protein) or n (nucleotide)",
+			},
+			&cli.DurationFlag{
+				Name:  "poll-interval",
+				Value: defaultPollInterval,
+				Usage: "How often to check job status",
+			},
+			&cli.DurationFlag{
+				Name:  "timeout",
+				Value: defaultTimeout,
+				Usage: "Maximum time to wait for a single job",
+			},
+			&cli.IntFlag{
+				Name:    "concurrency",
+				Aliases: []string{"c"},
+				Value:   defaultConcurrency,
+				Usage:   "Maximum number of concurrent InterProScan jobs",
+			},
+		},
+		Action: interpro.ConcurrentScan,
 	}
 }